Comment on "Which of the following programming language is best for a bioinformatics beginner?"
...o use R, as it has a lot of helpful packages and procedures. Here is manual, hope you find it useful: http://manuals.bioinformatics.ucr.edu/home/ht-seq3530 days ago
Comment on "Commercial and public next-gen-seq (NGS) software"
HiChIP: a high-throughput pipeline for integrative analysis of ChIP-Seq data http://www.biomedcentral.com/1471-2105/15/280/abstract3547 days ago
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Comment on "Next generation sequencing in R or bioconductor environment"
R package SPP for chip-seq analysis. It can read quite a few aligner's outp...http://compbio.med.harvard.edu/Supplements/ChIP-seq/tutorial.htmlHere is my versi...omed/SRAdb: query and use public next-generation sequencing data from within Rhttp...3621 days ago
Comment on "R and Bioconductor Tutorial"
R and Bioconductor for NGS data analysis http://master.bioconductor.org/help/course-materials/2012/CSC2012/Bioconductor-tutorial.pdf http://manuals.bioinformatics.ucr.edu/home/ht-seq3645 days ago
Comment on "List of popular bioinformatics software/tools"
TopHat http://tophat.cbcb.umd.edu/manual.shtml is a program that aligns RNA-Seq reads to a genome in order to identify exon-exon splice junctions. It is built on the ultrafast short read mapping program Bowtie.3647 days ago
Comment on "R and Bioconductor Tutorial"
...attern searches [1] Biostrings – Reading sequences in R [2] BSGenomes &nd...mplete genomes and BioC annotation data [3] DEGSeq – Identify differential...rface to online and other genome browsers. chipseq & ChIPpeakAnno – Ch...3669 days ago
Comment on "PLOS Computational Biology: Translational Bioinformatics educational resources"
Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.10033263813 days ago